view repmatch_gff3.xml @ 1:8159aaa7da4b draft

Uploaded

<?xml version="1.0"?>
<tool id="repmatch_gff3" name="RepMatch" version="@WRAPPER_VERSION@.0">
    <description>Match paired peaks from two or more replicates</description>
    <macros>
        <import>repmatch_gff3_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command>
        python $__tool_directory__/repmatch_gff3.py
        #for $i in $input:
             --input "${i}" "${i.hid}"
        #end for
        --method $method
        --distance $distance
        --step $step
        --replicates $replicates
        --low_limit $low_limit
        --up_limit $up_limit
        --output_files $output_files_cond.output_files
        --output_summary "$output_summary"
        #if str($output_files_cond.output_files) in ["all", "simple_orphan"]:
            --output_orphan "$output_orphan"
        #end if
        #if str($output_files_cond.output_files) =="all":
            --plot_format $output_files_cond.plot_format
            --output_detail "$output_detail"
            --output_key "$output_key"
            --output_histogram "$output_histogram"
        #end if
    </command>
    <inputs>
        <param  name="input" type="data" format="gff" multiple="True" min="2" label="Match paired peaks on" />
        <param name="method" type="select" label="Method of finding match">
            <option value="closest" selected="True">Closest</option>
            <option value="largest">Largest</option>
            <option value="all">All</option>
        </param>
        <param name="distance" type="integer" value="50" min="0" label="Maximum distance between peaks in different replicates to allow merging" />
        <param name="step" type="integer" value="0" min="0" label="Step size" help="Distance for each iteration" />
        <param name="replicates" type="integer" value="2" min="2" label="Minimum number of replicates that must be matched for merging to occur" />
        <param name="low_limit" type="integer" value="-1000" label="Lower limit for Crick-Watson distance filter" />
        <param name="up_limit" type="integer" value="1000" label="Upper limit for Crick-Watson distance filter" />
        <conditional name="output_files_cond">
            <param name="output_files" type="select" label="Restrict output to" help="Statistics will always be generated." >
                <option value="all" selected="True">no restrictions (output everything)</option>
                <option value="simple">matched pairs only</option>
                <option value="simple_orphan">matched pairs and orphans only</option>
            </param>
            <when value="simple" />
            <when value="simple_orphan" />
            <when value="all">
                <param name="plot_format" type="select" label="Output format for graph">
                    <option value="pdf" selected="True">Pdf</option>
                    <option value="png">Png</option>
                    <option value="svg">Svg</option>
                </param>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="output_summary" format="gff" label="Matched pairs: ${tool.name} on ${on_string}" />
        <data name="output_orphan" format="tabular" label="Orphans: ${tool.name} on ${on_string}">
            <filter>output_files_cond["output_files"] in ["all", "simple_orphan"]</filter>
       </data>
        <data name="output_detail" format="tabular" label="Details: ${tool.name} on ${on_string}">
            <filter>output_files_cond["output_files"] == "all"</filter>
       </data>
        <data name="output_key" format="tabular" label="Key: ${tool.name} on ${on_string}">
            <filter>output_files_cond["output_files"] == "all"</filter>
       </data>
        <data name="output_histogram" format="pdf" label="Histogram: ${tool.name} on ${on_string}">
            <filter>output_files_cond["output_files"] == "all"</filter>
            <actions>
                <action type="format">
                    <option type="from_param" name="output_files_cond.plot_format" />
                 </action>
           </actions>
       </data>
    </outputs>
    <tests>
        <param name="input" value="closest_s_input1.gff" ftype="gff" />
        <param name="input" value="largest_s_input1.gff" ftype="gff" />
        <param name="method" value="closest" />
        <param name="distance" value="50" />
        <param name="step" value="0" />
        <param name="replicates" value="2" />
        <param name="low_limit" value="-1000" />
        <param name="up_limit" value="1000" />
        <param name="output_files" value="all" />
        <param name="plot_format" value="png" />
        <output name="output_summary" file="summary_out1.gff" ftype="gff" />
        <output name="output_orphan" file="orphan_out1.tabular" ftype="tabular" />
        <output name="output_detail" file="orphan_detail1.tabular" ftype="tabular" />
        <output name="output_key" file="key_out1.tabular" ftype="tabular" />
        <output name="output_histogram" file="histogram_out1.pdf" ftype="pdf" compare="sim_size" />
    </tests>
    <help>
**What it does**
<![CDATA[

Replicate matching - matches paired peaks from two or more replicates, and produces a list of matched
groups and optionally a list of matched orphans.  Additional optional outputs include the median read
count for each input, details and a histogram.

]]>

**Options**

* **Method** - Method to use when calling replicates.
* **Distance** - Maximum distance between peaks in different replicates to allow merging.
* **Step Size** - Distance for each iteration.
* **Replicates** - Minimum number of replicates to call a peak.  Number of replicates required must be at least 2.
* **Lower Limit** - Lower limit for the Crick-Watson distance filter.
* **Upper Limit** - Upper limit for the Crick-Watson distance filter.
* **Plot Format** - Output format for graph.  The options are PNG or SVG.
    </help>
    <expand macro="citations" />
</tool>